[ensembl-dev] Changes to COSMIC data storage in ensembl API?

[Stefano Giorgetti]

Hello Jon,

The code base hasn't changed significantly transitioning from E!108 to 
E!109, TBH.

I tried (sort of) your code below, and I could get some IDs back from 
the API.

Possible differences between our code do not seem enough to explain why 
you are not retrieving any data:

  * Used "ensembldb.ensembl.org" host
  * Focussed on region chr18 between 49481681 and 49492479
  * returned the first 5 IDs

As additional note, I would check

 1. you are not connecting to our former US West mirror (which should
    not be the case)
 2. you may want to use
    "$slice->get_all_somatic_VariationFeatures_by_source('COSMIC')"
    instead of "get_all_somatic_VariationFeatures()"
    I am getting 6-fold increase in performance ... if you are
    interested only in COSMIC variants, of course

Is it maybe region-specific issue?
Feel free to share the regions you are interested in, should you want me 
to double check.

Hope this helps

Cheers,

Stefano

On 13/02/2023 14:40, Williams, Jonathan (RTH) OUH wrote:
>
> Hello All,
>
> As part of a pipeline, I’ve been using the following code snippet to 
> grab COSMIC variant IDs from specific regions of the human genome – 
> this all worked wonderfully until the beginning of February this year 
> and I’m wondering if the code base has changed with the most recent 
> ensembl release? Any advice on how to do this now, bearing in mind I 
> am definitely a bit of a Bioinformatics amateur?
>
> my $slice_adaptor = $registry->get_adaptor('Human', 'Core', 'Slice');
>
> my $slice = $slice_adaptor->fetch_by_region($coords);
>
> my $vs = $slice->get_all_somatic_VariationFeatures();
>
> my @variants = @{$vs};
>
> foreach (@variants){
>
>                 my $name = $_->name();
>
>                 push (@variant_list, $name);
>
> };
>
> When this was working the end result was pushing of COSV IDs into the 
> final @variant_list array which I was then able to print against 
> regions in a final report. This array now ends up empty so either the 
> “->name()” parameter or something to do with COSMIC data storage 
> amongst the “get_all_somatic_VariationFeatures” dataset may have been 
> altered…
>
> Jon Williams
>
>
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